Copper coin doctoring is a controversial subject that cuts at the roots of the hobby. It's become more deceptive, though much less prevalent, with the advancement of time and methods. But the motives have always been the same: increase the immediate worth of a coin by artificially enhancing its physical appearance. 
  
   The early years of Indian cent doctoring were the mid-1960s when several dealers made a practice of treating XF-AU examples through dipping to make them appear Uncirculated. Until that point the series enjoyed a large, devoted following. Passed on to the market at cheap prices, these pieces eventually degenerated in appearance as their new "skins" reacted over time, resulting in unnatural tones and lustre. Methods of treatment advanced over the years and resulted in a gradual loss of the collector base. Many of these coins can still be seen today in raw auction lots, especially on Ebay, or in substandard certified holders like ACG. The following link compares the look of more obviously dipped Indian cents compared to their original counterparts of the same date:
  
   When certified grading was born in 1986 it marked the first step in the recovery, but it wasn't until the late 1990's that prices in the Indian cent denom caught up with the rest of the market. PCGS and NGC began to restore the collector's faith in originality. But even PCGS, who are borderline paranoid about any unusual color since they guaranty copper (which costs them about $20,000 a month), faces new challenges in the 21st century.
   The early years of copper doctoring involved more primitive methods that were easy to detect once collectors were enlightened. They involved dipping which is visibly different than mechanical alterations such as polishing or buffing. Dipping allowed high relief areas to be cleaned uniformly with the fields by using chemicals that removed the thin outer skin of the coin, giving it an immediate brighter and cleaner look. But the original lustre and flow lines were stripped away along with the skin, and the new surface usually reacted quickly to the elements creating an unnatural tone. This technique is still used today in a lesser degree, but the process has been improved and is more difficult to detect.
   The recipe for state-of-the-art copper retoning isn't shared for obvious reasons. The few who fool PCGS and NGC with any degree of regularity operate best on the fringes of the business, and those dealers who are aware of them use their best business instincts by not discussing it in any detail. After all, the worst by-product of the few doctored coppers that pass the major grading services these days it not the coins themselves, but the shadow of doubt it casts on the vast majority of original ones.
   The code of silence is such that it's difficult to even prove it exists. After all, if a coin passes through the professional graders at PCGS as original, how is your average collector to declare otherwise? But even Q. David Bowers writes*:
            "Concerning MS-65 RD I think there is no rule about 'original' vs. recolored, and I'm not sure the difference can be ascertained in all instances.
            Among certified coins of the various services, it seems that 'mistakes', obviously retoned coins, etc., tend to 'stay' in their holders. This is why we spend a lot of time cherry-picking for quality. As I have written many times, one number does not fit all. And, among copper coins, you could take 20 'MS-65' certified large cents, with 'RD' surfaces, and there are some I would not buy at all (unless at an EF or AU price), and others that are true gems...
            ...I think the conclusion of this is the recurring theme, often voiced here and also when old-time numismatists gather, that certification services are just the BEGINNING for the evaluation of a coin."
    David Bowers also mentions in this Question And Answer Forum that some collectors have been able to track doctored certified coins. He mentions a knowledgable Lincoln collector who for years had been looking for a true original full mint red 1926-S MS65 cent, but had never seen one. Recently, some of the same pieces he had inspected earlier with red and brown surfaces have "become" gem red MS65.

   One of the advantages of the internet, and major dealer auction archives, is the ability to retrace the tracks of certain coins. While possible imaging differences make this unverifiable proof, there are some examples whose grade jump combined with the before/after images make their past extremely suspect. The following link is an example I found of an 1873 closed 3 Indian cent, PCGS MS64RB, that was transformed into a PCGS MS65RD coin:
The Dark Ages
The Certified Grading Period
The Present
Tracking Coins
   This is one of the more conclusive examples I've come across. I've found several others over the past year I'm more skeptical about due to their smaller, less detailed images and/or more ambiguous shared hallmarks. What this example proves is, while the color of a copper coin may change, distinguishing surface marks do not. Be careful not to confuse these post-mint acquired marks with common die traits many coins share because they were struck from the same die pair.
Conclusion
   My own observations combined with others whose opinion I value make me fairly certain a very sophisticated method of copper retoning exists today that sometimes fools the experts. But it's practiced on a very small scale, perhaps only perfected by one or two individuals. Like the two examples I shared, their main targets are key date/varieties that earn the greatest profit for their handywork if they upgrade by a single point and/or "advance" from RB to RD.
   This is only an opinion and should not be taken as anything more. Absolute proof is virtually impossible without the smoking gun. The best evidence I can provide as a "non-insider" are some very well matched footprints.
   Ways to arm yourself against purchasing doctored coppers include:
  studying your specialty so you know the good from the questionable
  stick with older slabs since even the more sophisticated doctoring methods may "turn"          in their slabs over time
  know the pedigree of high priced examples purchased
  buy only from dealers you know enforce all the above criteria
  buy only PCGS slabs since they guaranty copper color attribution
  use online auction archives, like Heritage and Goldberg, to research past sales
  stick with RB coppers, an option gem RD lovers don't need to resort to if they buy wisely 
* From Bowers and Merena's Rare Coin Review #147, 5/02